Lightnews — Scholar-powered news

Nick Loman @pathogenomenick.bsky.social · 4h

Love this!

Reposted by Nick Loman

Alan McNally @alanmcn1.bsky.social · 1d

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research

microbiologysociety.org/news/society...

<i>Microbial Genomics </i> Deputy Editor-in-Chief: Call for Expressions of interest

microbiologysociety.org

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Reposted by Nick Loman

Esther Schindler @estherschindler.bsky.social · 1d

I just saw someone use the abbreviation “AI;DR” and I’ll be laughing for a while.

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Reposted by Nick Loman

Adam Rawnsley @arawnsley.bsky.social · 3d

Was curious about JFK’s health so I asked google. TIL he was pregnant in 1960 but only put on 15-20lbs

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Reposted by Nick Loman

Sathnam Sanghera @sathnam.bsky.social · 5d

Please let this be true.

Have we passed peak social media? - on.ft.com/4pTb1Di via @FT

Have we passed peak social media?

As platforms degrade into outrage and slop, users are turning away

on.ft.com

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Reposted by Nick Loman

Dan Portik @dportik.bsky.social · 6d

New pre-print from the Banfield lab, highlighting an interesting case of 1.5Mb megaplasmids found in human gut.

Plasmid genomes were resolved using #PacBio HiFi sequencing with hifiasm-meta for #metagenome assembly. Host association was detected using epigenetic signals.

doi.org/10.1101/2025...

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae , a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplas...

doi.org

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Reposted by Nick Loman

Stephen Curry @scurry.bsky.social · 7d

As the @royalsociety.org council meets on 01 Oct to discuss the repudiation of its core values by one of its fellows, Elon Musk, I respectfully remind them of my proposals for actions that should help the RS recover its standing in the scientific community. occamstypewriter.org/scurry/2025/...

Conduct Unbecoming – how can the Royal Society escape its Musk box? | Reciprocal Space

occamstypewriter.org

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Reposted by Nick Loman

Larry Hunter @proflhunter.bsky.social · 8d

As a survivor of the last AI winter, I endorse Cory's take: "Plan for a future where you can buy GPUs for ten cents on the dollar...[and] there's a ton of extremely promising open source models that have barely been optimized and have vast potential for improvement." pluralistic.net/2025/09/27/e...

Pluralistic: The real (economic) AI apocalypse is nigh (27 Sep 2025) – Pluralistic: Daily links from Cory Doctorow

pluralistic.net

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Reposted by Nick Loman

Tami Lieberman @contaminatedsci.bsky.social · 8d

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

www.biorxiv.org

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Reposted by Nick Loman

Phase Genomics @phasegenomics.bsky.social · 8d

In this great new paper, the authors use metagenomic Hi-C to show that #phage with broad host range are fairly common, contrary to the prevailing view on their biology. Cutting edge methods like Hi-C are shedding light on our blind spots in the microbial world.

Phages with a broad host range are common across ecosystems - Nature Microbiology

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

www.nature.com

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Reposted by Nick Loman

Joseph Cherabie MD MSc (They/He) @jncherabiemd.bsky.social · 8d

And the CDC has officially decided to switch back from Mpox to Monkeypox. A reminder, the world still uses Mpox, this disease does not come from monkeys, Mpox is less stigmatizing and racist. Switching back is just meaningless, unnecessary, racist, and homophobic.

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Reposted by Nick Loman

Katie Martin @katie0martin.ft.com · 10d

We worry about Very Online Kids much more than their Very Online Parents, and I'm not sure that's wise

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Reposted by Nick Loman

Deena Mousa @deenamousa.com · 12d

In 2016 Geoffrey Hinton said “we should stop training radiologists now" since AI would soon be better at their jobs.

He was right: models have outperformed radiologists on benchmarks for ~a decade.

Yet radiology jobs are at record highs, with an average salary of $520k.

Why?

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Reposted by Nick Loman

Jeffrey Barrett @jeffbarrett.eu · 13d

The science is, in fact, clear. Good studies [1] consistently show a weak association between tylenol & autism. Those studies are very careful to say they can't establish whether this is causal. A huge Swedish study used a clever sibling design to address this, and showed zero causal effect [2].

NPR @npr.org · 14d

The science on Tylenol and autism isn't clear, despite President Trump's claims. Here's what parents need to know to make their own decisions about acetaminophen.

When it comes to Tylenol, what are parents to do?

The science on Tylenol and autism isn't clear, despite President Trump's claims. Here's what parents need to know to make their own decisions about acetaminophen.

n.pr

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Reposted by Nick Loman

Susan Kaye Quinn is Writing Solarpunk 🌞🌱 @susankayequinn.bsky.social · 13d

They've lost the 9yos

JA Westenberg
@Daojoan@mastodon.social

My 9 year old and his classmates have started using “that’s AI” to mean “I don’t believe you.”

Me: we’re having dinosaur meat for dinner

Kiddo: that’s AI
Sep 24, 2025, 07:36 AM

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Nick Loman @pathogenomenick.bsky.social · 13d

How many shopping days til Xmas

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Reposted by Nick Loman

Anna Cusco @annacusco.bsky.social · 15d

Finally, the results of my postdoc at the
@bigdatabiology.bsky.social lab in Shanghai see the light! The work includes my three favorite things research-wise: 🦠 microbiome, 🧬 long-reads, and 🐶 dogs.

See our new preprint:
www.biorxiv.org/content/10.1...

Capturing global pet dog gut microbial diversity and hundreds of near-finished bacterial genomes by using long-read metagenomics in a Shanghai cohort

Pet dogs are considered part of the family, and understanding their gut microbiomes can provide insights into both animal and household health. Most comprehensive studies, however, relied on short-rea...

www.biorxiv.org

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Reposted by Nick Loman

Joshua Weitz @joshuasweitz.bsky.social · 15d

Reminder: a large (2.5M+) sibling control study found "no evidence of increased risk of autism, ADHD, or intellectual disability associated with acetaminophen use". Precisely the kind of data that requires serious consideration before declaring mission accomplished.

jamanetwork.com/journals/jam...

Acetaminophen Use During Pregnancy and Children’s Risk of Autism, ADHD, and Intellectual Disability

This nationwide cohort study with sibling control analysis examines the association of acetaminophen use during pregnancy with children’s risk of autism, ADHD, and intellectual disability.

jamanetwork.com

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Nick Loman @pathogenomenick.bsky.social · 15d

The scariest bit was when Chris cycled through London with his kids

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Reposted by Nick Loman

Greg Fell @felly500.bsky.social · 15d

www.sciencemediacentre.org/expert-react...

Hard to know what to say really
Fortunately Sci Media Centre is on hand....

@sciencemediacentre.bsky.social

expert reaction to media reports that the Trump administration will link paracetamol to autism | Science Media Centre

www.sciencemediacentre.org

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Reposted by Nick Loman

Medical Research Foundation @medresfdn.bsky.social · 15d

See our ELP winner Dr Joe Grove discussing his work with Dr Chris van Tulleken at 9pm tonight on BBC2, or right now on BBC iPlayer: bbc.in/47WjAXM

Joe and his team at @cvrinfo.bsky.social @uofglasgow.bsky.social are using #AI to better understand how viruses evolve and function.

Drs Chris van Tulleken and Joe Grove are sitting in front of a computer screen which is displaying a model of a virus protein. Joe is pointing at the model onscreen, explaining its significance to Chris.

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Reposted by Nick Loman

Ben Vezina @bananabenana.bsky.social · 15d

Automated, almost-error-free consensus #assemblies with Autocycler

Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome

Once again, incredible, landmark work from @rrwick.bsky.social

doi.org/10.1093/bioi...

Tool here: github.com/rrwick/Autoc...

#bioinformatics #genomics

Box and whisker plot of various assemblers and their number of errors per assembly. Autocycler outperforms all assemblers with the lowest median of <=10 errors per genome

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Nick Loman @pathogenomenick.bsky.social · 15d

Yep. Capitalism is to blame I guess. Theres also an environmental argument to be made for keeping (some) kit running as long as possible.

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Nick Loman @pathogenomenick.bsky.social · 15d

You could - that is true - but then the Uni also charge all those ‘lab overheads’ at the same time

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Nick Loman @pathogenomenick.bsky.social · 15d

I would be in favour for a basic right to repair rule for lab kit - eg I would rather not take out a $4k service contract to pay for the cost of repairing a $10 sensor which isn’t available to buy as a part.

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